def test_check_geospatial_vars_have_attrs(self):
# create geophysical variable
ds = MockTimeSeries() # time, lat, lon, depth
temp = ds.createVariable("temp", np.float64, dimensions=("time", ))
# should fail here
results = self.ioos.check_geospatial_vars_have_attrs(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# should pass - default_fill_value sets _FillValue attr
ds = MockTimeSeries(
default_fill_value=9999999999.0) # time, lat, lon, depth
ds.variables["time"].setncattr("standard_name", "time")
ds.variables["time"].setncattr(
"standard_name_url",
"http://cfconventions.org/Data/cf-standard-names/64/build/cf-standard-name-table.html",
)
ds.variables["time"].setncattr("units",
"hours since 1970-01-01T00:00:00")
ds.variables["time"].setncattr("missing_value", 9999999999.0)
results = self.ioos.check_geospatial_vars_have_attrs(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
def test_check_standard_name(self):
ds = MockTimeSeries() # time, lat, lon, depth
# no standard names
results = self.ioos.check_standard_name(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# give standard names to all variables
ds.variables["time"].setncattr("standard_name", "time")
ds.variables["lon"].setncattr("standard_name", "longitude")
ds.variables["lat"].setncattr("standard_name", "latitude")
ds.variables["depth"].setncattr("standard_name", "depth")
results = self.ioos.check_standard_name(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
# add a QARTOD variable, no standard name - should fail
qr = ds.createVariable("depth_qc", np.byte)
qr.setncattr("flag_meanings", "blah")
results = self.ioos.check_standard_name(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# bad standard name
qr.setncattr("standard_name", "blah")
results = self.ioos.check_standard_name(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# good standard name
qr.setncattr("standard_name", "spike_test_quality_flag")
results = self.ioos.check_standard_name(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
def test_check_geophysical_vars_have_attrs(self):
# create geophysical variable
ds = MockTimeSeries() # time, lat, lon, depth
temp = ds.createVariable("temp", np.float64, dimensions=("time", ))
# should fail here
results = self.ioos.check_geophysical_vars_have_attrs(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# set the necessary attributes
ds = MockTimeSeries(
default_fill_value=9999999999.0) # time, lat, lon, depth
temp = ds.createVariable("temp", np.float64,
fill_value=9999999999.0) # _FillValue
temp.setncattr("missing_value", 9999999999.0)
temp.setncattr("standard_name", "sea_surface_temperature")
temp.setncattr(
"standard_name_url",
"http://cfconventions.org/Data/cf-standard-names/64/build/cf-standard-name-table.html",
)
temp.setncattr("units", "degree_C")
temp.setncattr("platform", "myPlatform")
results = self.ioos.check_geophysical_vars_have_attrs(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
def test_check_accuracy(self):
ds = MockTimeSeries() # time, lat, lon, depth
temp = ds.createVariable("temp",
np.float64,
dimensions=("time", ),
fill_value=9999999999.0) # _FillValue
temp.setncattr("standard_name", "sea_water_temperature")
results = self.ioos.check_accuracy(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# add non-numeric vals for accuracy
# no gts_ingest attr, so only existence tested
temp.setncattr("accuracy", "bad")
results = self.ioos.check_accuracy(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
# add gts_ingest, accuracy should be numeric
temp.setncattr("gts_ingest", "true")
temp.setncattr("standard_name", "sea_water_practical_salinity")
temp.setncattr("accuracy", "45")
results = self.ioos.check_accuracy(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# add numeric for accuracy
temp.setncattr("gts_ingest", "true")
temp.setncattr("standard_name", "sea_water_practical_salinity")
temp.setncattr("accuracy", 45)
results = self.ioos.check_accuracy(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
def test_check_instrument_variables(self):
ds = MockTimeSeries() # time, lat, lon, depth
# no instrument variable, should pass
results = self.ioos.check_instrument_variables(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
temp = ds.createVariable("temp", np.float64, dimensions=("time",))
temp.setncattr("cf_role", "timeseries")
temp.setncattr("standard_name", "sea_surface_temperature")
temp.setncattr("units", "degree_C")
temp.setncattr("axis", "Y")
temp.setncattr("instrument", "myInstrument")
temp[:] = 45.0
instr = ds.createVariable("myInstrument", np.float64, dimensions=("time",))
# give instrument variable with component
instr.setncattr("component", "someComponent")
results = self.ioos.check_instrument_variables(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
# give discriminant
instr.setncattr("discriminant", "someDiscriminant")
results = self.ioos.check_instrument_variables(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
# bad component
instr.setncattr("component", 45)
results = self.ioos.check_instrument_variables(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
def test_check_qartod_variables_references(self):
ds = MockTimeSeries() # time, lat, lon, depth
# no QARTOD variables
results = self.ioos.check_qartod_variables_references(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
# QARTOD variable without references (fail)
qr = ds.createVariable("depth_qc", np.byte)
qr.setncattr("flag_meanings", "blah")
qr.setncattr("standard_name", "spike_test_quality_flag")
results = self.ioos.check_qartod_variables_references(ds)
self.assertFalse(all(r.value for r in results))
# QARTOD variable with references (pass)
qr.setncattr("references", "http://services.cormp.org/quality.php")
results = self.ioos.check_qartod_variables_references(ds)
self.assertTrue(all(r.value for r in results))
self.assertEqual(results[0].msgs, []) # only one Result to test
# QARTOD variable with bad references (fail)
qr.setncattr("references",
r"p9q384ht09q38@@####???????////??//\/\/\/\//\/\74ht")
results = self.ioos.check_qartod_variables_references(ds)
self.assertFalse(all(r.value for r in results))
def test_check_contributor_role_and_vocabulary(self):
ds = MockTimeSeries()
# no values, fail
results = self.ioos.check_contributor_role_and_vocabulary(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# valid role, no vocab, fail
ds.setncattr("contributor_role", "editor")
results = self.ioos.check_contributor_role_and_vocabulary(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# valid role, valid vocab, pass
ds.setncattr(
"contributor_role_vocabulary",
"https://vocab.nerc.ac.uk/collection/G04/current/",
)
results = self.ioos.check_contributor_role_and_vocabulary(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
# one valid role, one valid vocab, should fail
ds.setncattr("contributor_role", "editor,notvalid")
ds.setncattr(
"contributor_role_vocabulary",
"https://vocab.nerc.ac.uk/collection/G04/current/,notvalid",
)
results = self.ioos.check_contributor_role_and_vocabulary(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# both valid
ds.setncattr("contributor_role", "editor,coAuthor")
ds.setncattr(
"contributor_role_vocabulary",
"https://vocab.nerc.ac.uk/collection/G04/current/,https://www.ngdc.noaa.gov/wiki/index.php?title=ISO_19115_and_19115-2_CodeList_Dictionaries#CI_RoleCode",
)
results = self.ioos.check_contributor_role_and_vocabulary(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
# bad value type
ds.setncattr("contributor_role", 21)
results = self.ioos.check_contributor_role_and_vocabulary(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
ds.setncattr("contributor_role", "editor,coAuthor")
ds.setncattr("contributor_role_vocabulary", 64)
results = self.ioos.check_contributor_role_and_vocabulary(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
def test_check_instrument_make_model_calib_date(self):
"""
Per the IOOS-1.2 spec, instrument variables should have
make_model and calibration_date attributes.
"""
ds = MockTimeSeries() # time, lat, lon, depth
results = self.ioos.check_instrument_make_model_calib_date(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
# make an instrument variable
temp = ds.createVariable("temperature", "d", dimensions=("time", ))
temp.setncattr("instrument", "inst")
inst = ds.createVariable(
"inst", "d", dimensions=()) # no make_model or calibration_date
results = self.ioos.check_instrument_make_model_calib_date(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# add make_model
inst.setncattr("make_model", "yessir")
results = self.ioos.check_instrument_make_model_calib_date(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
# add calibration_date
inst.setncattr("calibration_date", "2020-08-19") # not ISO, fail
results = self.ioos.check_instrument_make_model_calib_date(ds)
scored, out_of, messages = get_results(results)
self.assertLess(scored, out_of)
inst.setncattr("calibration_date", "2020-08-19T00:00:00") # ISO, pass
results = self.ioos.check_instrument_make_model_calib_date(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
def test_check_qartod_variables_flags(self):
ds = MockTimeSeries() # time, lat, lon, depth
# no QARTOD variables
results = self.ioos.check_qartod_variables_flags(ds)
scored, out_of, messages = get_results(results)
self.assertEqual(scored, out_of)
# QARTOD variable without flag_values, flag_meanings (fail)
qr = ds.createVariable("depth_qc", np.byte)
qr.setncattr("standard_name", "spike_test_quality_flag")
results = self.ioos.check_qartod_variables_flags(ds)
self.assertTrue(not any(r.value for r in results)) # all False
# QARTOD variable with flag meanings, without flag_meanings
qr.setncattr("flag_values", np.array([0, 1, 2], dtype=np.byte))
results = self.ioos.check_qartod_variables_flags(ds)
self.assertEqual(results[0].value[0],
results[0].value[1]) # should pass
self.assertFalse(results[1].value) # still fail
# QARTOD variable with flag meanings, flag_values
qr.setncattr("flag_meanings", "x y z") # alphanumeric, space-separated
results = self.ioos.check_qartod_variables_flags(ds)
self.assertEqual(results[0].value[0], results[0].value[1]) # pass
self.assertEqual(results[1].value[0], results[1].value[1]) # pass
# flag_values array not equal to length of flag_meanings
qr.setncattr("flag_values", np.array([0, 1], dtype=np.byte))
results = self.ioos.check_qartod_variables_flags(ds)
self.assertLess(results[0].value[0],
results[0].value[1]) # should fail
self.assertEqual(results[1].value[0], results[1].value[1]) # pass
# flag_values right length, wrong type
qr.setncattr("flag_values", np.array([0, 1, 2], dtype=np.float64))
results = self.ioos.check_qartod_variables_flags(ds)
self.assertLess(results[0].value[0],
results[0].value[1]) # should fail
self.assertEqual(results[1].value[0], results[1].value[1]) # pass
